Closed bschilder closed 2 years ago
Ok, this is indeed triggered by liftover()
here:
https://github.com/neurogenomics/MungeSumstats/blob/021f36322101e8b5dbc796fd03a2fad3795f4dae/R/format_sumstats.R#L896
I believe this is happening because the target genome build is being supplied as NULL
.
This corresponds to the convert_ref_genome
argument.
I guess one solution would be to have an early check inn format_sumstats
for the convert_ref_genome
parameter and when it's NULL
, set it to some genome ref version and send a message to the user.
Found the issue - I just needed to add a check to see if the user even wanted the genome build converted before running the checks to see if it needs to be inferred. This is updated in 1.5.6 (will push today)
Just a note to myself to look into this message that comes up (but doesn't seem to cause an error).
Reprex
Data
Download the file plt.assoc from here: ftp://ftp.sanger.ac.uk/pub/project/humgen/summary_statistics/UKBBblood cell_traits/
Code
Output messages
Session info